Contacts of the helix formed by residues 50 - 62 (chain B) in PDB entry 2W99
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.9 23.3 - - + -
40B PRO* 3.3 37.2 - - + +
48B GLY 3.3 2.4 - - - +
49B LEU* 1.3 82.9 - - + +
51B ILE* 1.3 59.6 + - + +
52B SER* 2.9 4.7 - - - +
53B THR* 2.8 46.3 + - - +
54B VAL* 3.1 14.0 + - - +
87B ILE* 4.7 1.3 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 3.0 54.7 - - + +
118A PRO* 4.2 12.6 - - + -
44B GLU* 4.4 13.7 - - + +
49B LEU 3.4 2.7 - - - +
50B PRO* 1.3 71.3 - - + +
52B SER* 1.3 55.2 + - - +
54B VAL* 3.2 5.6 - - - +
55B ARG* 2.8 81.2 + - - +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 2.9 4.8 - - - +
51B ILE* 1.3 78.8 + - - +
53B THR* 1.3 57.0 - - - +
55B ARG* 4.0 8.9 - - - +
56B GLU* 2.8 42.3 + - - +
163B ARG* 6.0 4.3 - - - -
164B ILE* 5.6 0.6 - - - -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 3.9 21.3 - - + -
39B VAL* 3.5 33.8 - - + +
49B LEU* 5.6 0.4 - - + -
50B PRO* 2.8 31.1 + - + +
52B SER* 1.3 79.2 - - - +
54B VAL* 1.3 65.9 + - + +
55B ARG 3.2 0.2 - - - -
56B GLU* 4.0 2.2 - - - +
57B VAL* 3.0 34.0 + - + +
89B VAL* 5.1 4.7 - - + -
164B ILE* 4.8 14.3 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 5.6 4.3 - - + +
112A LYS* 4.2 21.1 - - + -
113A MET* 4.0 13.6 - - + +
141A GLU* 4.8 0.4 - - - +
145A VAL* 5.8 1.6 - - + -
150A TRP* 3.9 13.1 - - + -
152A LEU* 4.7 10.6 - - + +
49B LEU* 3.4 38.8 - - + +
50B PRO 3.1 14.8 - - - +
51B ILE* 3.2 15.3 - - - +
53B THR* 1.3 75.4 - - - +
55B ARG* 1.3 68.2 + - + +
57B VAL* 4.3 0.5 - - - +
58B ALA* 2.9 33.5 + - - +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS 2.3 33.2 + - - +
113A MET* 4.1 28.7 + - + +
114A LYS 4.9 0.2 - - - -
115A GLU 3.2 26.2 + - - +
116A THR* 4.8 4.8 + - - +
118A PRO* 4.2 5.9 - - - +
51B ILE* 2.8 45.0 + - - +
52B SER* 4.3 7.1 - - - +
53B THR 3.2 0.6 - - - -
54B VAL* 1.3 89.6 - - + +
56B GLU* 1.3 63.9 + - + +
58B ALA* 3.6 1.6 - - - +
59B LEU* 3.2 33.0 + - + +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER* 2.8 29.2 + - - +
53B THR 4.0 0.7 - - - +
55B ARG* 1.3 76.2 - - + +
57B VAL* 1.3 66.5 + - - +
59B LEU* 3.3 22.9 + - - +
60B LEU* 3.3 17.5 + - - +
160B GLY* 6.1 0.7 - - - -
163B ARG* 3.1 54.8 + - + +
164B ILE* 3.3 24.9 - - + +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TRP* 3.4 45.5 - - + +
53B THR* 3.0 26.0 + - + +
56B GLU* 1.3 75.1 - - - +
58B ALA* 1.3 65.7 + - - +
60B LEU* 3.0 17.1 + - - +
61B ARG* 3.2 11.3 + - + +
74B LEU* 4.4 2.2 - - + -
77B VAL* 3.7 20.6 - - + -
89B VAL* 5.2 2.0 - - + -
91B LEU* 4.0 18.4 - - + -
164B ILE* 3.6 24.0 - - + -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 3.8 26.5 - - + -
150A TRP 3.5 18.1 - - - +
151A ASN* 5.3 0.2 - - - +
152A LEU* 4.3 5.5 + - + -
153A ALA* 4.1 15.2 + - + +
54B VAL 2.9 22.4 + - - +
55B ARG 3.6 4.9 - - - +
57B VAL* 1.3 77.9 - - - +
59B LEU* 1.3 57.5 + - - +
61B ARG* 3.2 7.1 + - - +
62B ARG* 3.0 23.2 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 5.5 3.4 - - + -
153A ALA* 4.1 19.1 - - + -
55B ARG* 3.2 17.6 + - + +
56B GLU* 3.6 19.7 - - - +
57B VAL 3.1 0.6 - - - -
58B ALA* 1.3 75.1 - - + +
60B LEU* 1.3 62.6 + - + +
62B ARG* 2.9 53.1 + - - +
63B LEU* 3.7 4.1 - - - +
134B ASN 5.9 2.2 - - - +
136B ILE* 5.5 7.1 - - + +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU 3.3 12.3 + - - +
57B VAL 3.0 3.2 + - - +
59B LEU* 1.3 77.3 - - + +
61B ARG* 1.3 59.5 + - - +
63B LEU* 3.3 24.2 - - + +
64B GLU* 4.3 2.1 + - - +
74B LEU* 3.3 41.8 + - + +
91B LEU* 5.4 0.4 - - + -
93B PHE* 5.1 1.6 - - + -
136B ILE* 3.9 26.0 - - + -
159B PHE* 4.3 35.1 - - + +
160B GLY* 5.0 5.6 - - - -
161B LEU* 4.0 28.0 - - + +
164B ILE* 4.4 11.0 - - + -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 2.8 42.5 + - - +
150A TRP 3.4 21.5 - - - +
151A ASN* 4.0 33.3 - - - +
57B VAL* 3.2 13.0 + - + +
58B ALA 3.2 6.2 + - - +
59B LEU 3.1 0.6 - - - -
60B LEU* 1.3 74.7 - - - +
62B ARG* 1.3 51.3 + - - +
63B LEU 2.7 17.5 + - - -
64B GLU* 3.1 33.7 + - - +
65B ALA* 4.6 2.8 + - - +
74B LEU* 3.0 46.9 + - + -
75B MET 3.6 16.2 + - - -
76B ASP* 4.3 4.2 - - - +
77B VAL* 3.9 3.8 - - - -
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 6.0 8.3 - - + -
114A LYS* 4.8 9.1 - - - +
151A ASN* 4.8 3.2 + - - +
153A ALA* 3.4 42.7 + - + +
154A ALA 4.4 6.1 + - - -
155A MET* 5.2 9.1 - - - -
159A ASP* 5.3 4.0 + - - -
58B ALA 3.0 11.2 + - - +
59B LEU* 2.9 31.2 + - - +
61B ARG* 1.3 70.8 - - - +
63B LEU* 1.3 74.7 + - - +
65B ALA* 6.0 1.6 - - - -
66B PHE* 4.5 14.0 - - + -
134B ASN* 4.6 0.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il